D-Wave vs. MEP

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The main purpose of this site is to extend the intraoperative monitoring to include the neurophysiologic parameters with intraoperative navigation guided with Skyra 3 tesla MRI and other radiologic facilities to merge the morphologic and histochemical data in concordance with the functional data.
CNS Clinic
Located in Jordan Amman near Al-Shmaisani hospital, where all ambulatory activity is going on.
Contact: Tel: +96265677695, +96265677694.

Skyra running
A magnetom Skyra 3 tesla MRI with all clinical applications started to run in our hospital in 28-October-2013.
Shmaisani hospital
The hospital where the project is located and running diagnostic and surgical activity.

Tractography is a procedure to demonstrate the neural tracts. It uses special techniques of magnetic resonance imaging (MRI), and computer-based image analysis. The results are presented in two- and three-dimensional images. In addition to the long tracts that connect the brain to the rest of the body, there is a complicated 3D network formed by short connections among different cortical and subcortical regions. The existence of these bundles has been revealed by histochemistry and biological techniques on post-mortem specimens. Brain tracts are not identifiable by direct exam, CT, or MRI scans. This difficulty explains the paucity of their description in neuroanatomy atlases and the poor understanding of their functions.
The MRI sequences used look at the symmetry of brain water diffusion. Bundles of fiber tracts make the water diffuse asymmetrically in a tensor, the major axis parallel to the direction of the fibers. The asymmetry here is called anisotropy. There is a direct relationship between the number of fibers and the degree of anisotropy.

Diffusion tensor imaging (DTI) data has been used to seed various tractographic assessments of this patient's brain. These are seen in superior (A), posterior (B), and lateral views (C&D). The seeds have been used to develop arcuate and superior longitudinal fasciculi in (A) and (B), for brainstem, and corona radiata in (C), and as combined data sets in (D). Some of the two dimensional projections of the tractographic result are also shown. The data set may be rotated continuously into various planes to better appreciate the structure. Color has been assigned based on the dominant direction of the fibers. There is asymmetry in the tractographic fiber volume between the right and left arcuate fasciculus (Raf & Laf) (smaller on the left) and between the right and left superior longitudinal fasciculus (Rslf & Lslf) (smaller on the right). Also seen are Tapetum (Ta), Left corona radiata (Lcr) and Left middle cerebellar peduncle (Lmcp).

Tractographic reconstruction of neural connections via Diffusion tensor imaging (DTI).


Tractography and FA map superimposed on morphology with the syngo 3D Neuro Track Card

White matter fiber tracts seen with syngo DTI Tractography ( 256 diffusion directions)

White matter fiber tracts seen with syngo DTI Tractography ( 256 diffusion directions)

Tensor image of the brain at ventricular level

FA map generated with syngo DTI Tractography and inline function

FA map showing displacement of fiber tracks by intraventricular meningioma

MRI Technique

Tractography is performed using Diffusion Tensor Imaging, an MR technique which is sensitive to the diffusion of water in the body, and can be used to reveal its 3D shape. Free diffusion occurs equally in all directions. This is termed "isotropic" diffusion. If the water diffuses in a medium with barriers, the diffusion will be uneven, which is termed "anisotropic" diffusion. In such a case, the relative mobility of the molecules from the origin has a shape different from a sphere. This shape is often modeled as an ellipsoid, and the technique is then called Diffusion Tensor Imaging. Barriers can be many things--cell membranes, axons, myelin, etc; but in white matter the principal barrier is the myelin sheath of axons. Bundles of axons provide a barrier to perpendicular diffusion and a path for parallel diffusion along the orientation of the fibers.
Anisotropic diffusion is expected to be increased in areas of high mature axonal order. Conditions where the myelin or the structure of the axon are disrupted, such as trauma, tumors, and inflammation reduce anisotropy, as the barriers are affected by destruction or disorganization.
Anisotropy is measured in several ways. One way is by a ratio called "fractional anisotropy" (FA). An anisotropy of "0" corresponds to a perfect sphere, whereas 1 is an ideal linear diffusion. Well-defined tracts have FA larger than 0.20. Few regions have FA larger than 0.90. The number gives information of how aspherical the diffusion is but says nothing of the direction.
Each anisotropy is linked to an orientation of the predominant axis (predominant direction of the diffusion). Post-processing programs are able to extract this directional information.
This additional information is difficult to represent on 2D grey-scaled images. To overcome this problem a color code is introduced . Basic colors can tell the observer how the fibers are oriented in a 3D-coordinate system: This is termed an "anisotropic map". The software could encode the colors in this way:
Red indicates directions in the X axis: right to left or left to right.
Green indicates directions in the Y axis: posterior to anterior or from anterior to posterior.
Blue indicates directions in the Z axis: foot-to-head direction or vice versa
Notice that the technique is unable to discriminate the "positive" or "negative" direction in the same axis.


syngo DTI (Diffusion Tensor Imaging) Tractography
syngo DTI Tractography uses diffusion tensor data and allows 3D visualization of specific white matter tracts. For example, one can determine the location of the corticospinal tract or the thalamocortical tract with the help of syngo DTI Tractography.

Clinical Applications

Pre-operative planning with combination of tractography and functional MRI.
Brain tumor differentiation.
By combining ADC and anisotropy data, the severity of strokes can be assessed and acute-ischemic changes can be distinguished from chronic-ischemic changes.
Diagnosis and follow-up of MS lesions.
May be useful in evaluation of normal brain development and maturation.


Measurement of up to 256 directions of diffusion-weighting with up to 16 different b-values.
Inline processing of the Fractional Anisotropy (FA) maps, ADC maps and trace-weighted images based on the tensor.
3D syngo DTI Tractography data in color overlaid onto the anatomy with the syngo 3D Neuro Task Card allows easy navigation through the brain.

Additional Information

In the brain, the axons of neurons form fiber tracts which impose directionality (anisotropy) on measurements of water diffusion. The aggregate diffusion of water within these tracts is quantified at each point by the diffusion tensor. Multiple parameters can be derived from the diffusion tensor, including the trace, ADC (Apparent Diffusion Coefficient), the relative anisotropy, and the fractional anisotropy. These secondary parameters are independent of the frame of reference and are very sensitive to white matter pathology.

syngo DTI has optimized sequences for a complete description of the diffusion properties of the brain within the scope of the tensor diffusion model, both for anisotropic and isotropic diffusion which support excellent evaluation of diseases of the white matter. It is a post-processing tool for data obtained by syngo DTI Tractography and allows for quantitative evaluation of the rate and direction of water motion within a voxel, calculation of different diffusion parameters and visualization of colored diffusion tensor imaging maps like the Fractional Anisotropy maps. syngo DTI Evaluation also enables ROI-based evaluation of parameter images.

syngo DTI and syngo DTI Evaluation will help you identify anatomical substructures and with the help of fiber direction maps and fiber tracts (tractography) you will be able to assess the microstructural aspects of the brain lesions.

Step by step:

1. Load the 3D anatomy series and epi DTI Tensor datasets into the Neuro 3D Task-card. Use the Neuro 3D icon to load these series.
2. Open the display menu, and right click the clip plane icon. This will allow you to cut out portions of the head to visualize areas of interest.
3. Double click the 4th segment to enlarge the 3D anatomy image.
4. Activate the clip plane by left clicking its edge, then left click and hold to cut image to area of interest.
5. While holding the control key on the keyboard, left click and draw seed points over area where you wish to create tracts. Right click on seed points and select start Tractography.
6. The anatomic image can be rotated to better visualize tracts created by holding the left mouse key and moving in any direction.

Neuro fMRI/DTI Combi Package #T+D

The Neuro fMRI/DTI Combi Package is a bundle of:
- Inline BOLD Imaging :Performing a Motor Cortex Functional Exam
- 3D PACE syngo : Prospective Acquisition CorrEction 
- BOLD 3D Evaluation syngo
- fMRI Trigger Converter
- Diffusion Tensor Imaging
- DTI Evaluation
- DTI Tractography syngo

The bundle comprehends all acquisition and postprocessing tools for comprehensive BOLD fMRI and DTI exams. BOLD fMRI experiments can be displayed fused with DTI data and anatomy. The package is particularly valuable for presurgical planning. The 3D display of anatomical images, functional brain mapping results and DTI allows a better understanding of the spatial relationship between eloquent cortices, cortical landmarks, brain lesions and tract shifts of white matter.

Inline BOLD Imaging
The BOLD imaging package allows the user to define protocols which, apart from the measurement, configure automatic evaluation of the measured data during the scan. With Inline Technology it is thus possible to generate statistical images (t-value) based on 3D motion corrected and spatially filtered data automatically in real time without any further user interaction. The Inline display of activation cards allows the user to decide during the scan whether enough statistical power has built up for his brain mapping task or if the examination is corrupted by motion. As a result examinations will be shorter with a higher success rate. Functional brain mapping can be easily integrated into the clinical routine e.g. prior to neurosurgical interventions.

Additional Features:
- Inline retrospective 3D motion detection and correction in 3 rotational and 3 translational directions
- Inline t-statistics calculation for variable paradigms and display of t-value images
- Statistical evaluation by means of “General Linear Model (GLM)”:
- Paradigms can be configured
- Transitions between passive and active states can be modeled by the hemodynamic response function
- Correction of low-frequency trends
- Allows for time delays due to the BOLD-EPI slice order during a measurement
- Display of GLM design matrix
- Display of a continuously updated t-value card during measurement
- Display of colored activation cards continuously updated during measurement, overlaid over the respective BOLD images using Inline technology
- MOSAIC image mode for accelerating display, processing and storage of images

3D PACE syngo
By tracking the patients head 3D PACE reduces motion resulting in increased data quality beyond what can be achieved with a retrospective motion correction. As a result the sensitivity and specificity of BOLD experiments are increased.
- Real time prospective motion correction: Highest accuracy real time motion detection algorithm feeding a real time feed back loop to the acquisition system with updated positioning information
- 3D motion correction for 6 degrees of freedom (3 translation and 3 rotation)
- Motion related artifacts are avoided in first place instead of correcting for them retrospectively
- Significant reduction of motion-related artifacts in statistical evaluations
- Increased sensitivity and specificity of BOLD experiments

BOLD 3D Evaluation syngo
All tasks from statistical evaluation of the fMRI datasets to reading and exporting results are supported by BOLD 3D Evaluation syngo:

Generation of statistical maps:
- In cases an inline calculated statistical map is not available a statistical map can be generated easily using processing protocols. An intuitive editor UI allows the paradigm definition and offers the selection of head motion correction, image filters and statistical evaluation.
- Predefined processing protocols and paradigms are available, which can be edited if required.

Statistical evaluation using General Linear Model (GLM)
- Transitions between passive and active states modeled by the hemodynamic response function.
- Correction of low-frequency trends.
- Corrects for time delays due to the BOLD-EPI slice order during a measurement.
- Output of a t-value map and the GLM design matrix

Inline monitoring of the fMRI exam
- During an ongoing BOLD imaging exam results are calculated (by Inline BOLD imaging) and displayed in real time.
- The results are displayed and continuously updated as an overlay on online adjustable, free angulated cut planes through the anatomical 3D data set.
- The evolving signal time courses in task-related areas of activation can be displayed and monitored.

Visualization of fMRI Results
- Visualization with 3D volume rendering.
- Superimposing on cut planes through the volume.
- Interactive Navigation: Zoom, pan and rotate in 3D without noticeable delay. Free double oblique angulation of up to 6 cut planes.
- Cine display of the BOLD time series and of EPI volumes in 3 orthogonal cuts for evaluation of non-corrected head motion.

Data Quality Monitoring
- Based on the B0 field map, loaded automatically with the fMRI data, areas with less reliable results are indicated.

fMRI Trigger Converter
An optical trigger signal is available to trigger external stimulation devices in fMRI experiments.
With the "fMRI Trigger Converter" this signal can be converted to an electrical signal (TTL/BNC and RS 232 interface for PC; modes: toggle or impulse).

Diffusion Tensor Imaging
Diffusion Tensor Imaging allows for a complete description of the diffusion properties of the brain within the scope of the tensor diffusion model, both for anisotropic and isotropic diffusion. Efficient diffusion direction schemes are pre-defined to allow for optimal diffusion directional resolution. Schemes with up to 256 directions can be selected.
Inline technology enables automatic and immediate calculation of the diffusion tensor, including grey-scale and colored “fractional anisotropy" (FA) map derived from it.

- Measurements with up to 256 different directions and with up to 16 different b-values
- Inline calculation of tensor, grey-scale and colored FA map, ADC map and trace-weighted image
- Support of parallel imaging (iPAT)
- Clinical protocols with full head coverage, incl. inline calculation of tensor, FA, ADC and trace-weighted images in 4 minutes.

DTI Tractography syngo
syngo DTI Tractography is optimized for the clinical use by providing advanced 3D visualization of white matter tracts in the context of 2D or 3D anatomical datasets and DTI datasets. DTI data sets can be explored fast and intuitively using the interactive QuickTracking. QuickTracking instantaneously displays the tract originating from the mouse pointer position while moving over the DTI data set. This also allows identifying qualified regions to place seeding ROIs. Seed points can be set to assess connectivity by tracking with single ROI and with multiple ROIs. Furthermore they can be placed in fused views displaying the anatomical reference and e.g. the colored FA map simultaneously.
Texture Diffusion, a highly versatile in-plane visualization of white matter tracts, allows to display and read DTI Tractography results on PACS reading stations and in the OR.
At the same time the package provides the scientific user with the flexibility to configure the tracking algorithm and to change display settings for the tracts. Tract and seeding ROI statistics are included to support publications (e.g. mean/max FA value, min/mean/max ADC value).
All views can be exported as DICOM images or bitmaps. Tract and seeding ROI statistics can be exported as html files.

DTI Evaluation
Clinical applications are supported by a dedicated DTI evaluation mode to support diagnostics of white matter diseases (e.g. multiple sclerosis and brain maturation disorders). Based on the tensor, in addition to the already inline-calculated parameter maps, further maps characterizing the anisotropy of diffusion properties can be calculated and stored. Multiple diffusion parameter maps (e.g. Fractional Anisotropy, ADC, b=0) and an anatomical image are displayed next to each other in the same slice position for comparison. The images can be evaluated together based on ROIs and the results can be documented in a table. The display options include 2D and 3D tensor graphics, colour-coded images and overlay images on the anatomical images.

In addition, the package offers the scientific user full flexibility of 2- and 3-dimensional visualization of the diffusion tensor with measures of isotropic and anisotropic (fractional and relative) diffusion, Eigen vectors (E1, E2, E3) of the diffusion tensor and shape-descriptive measures of the diffusion tensor (linear, planar, spherical).

This is a neurosurgical site dedicated to intraoperative monitoring to catch in time the early signs of possible functional complications before they evolve to morphologic ones.

Complications in neurosurgery

So as to have a digital data, the best ever made Inomed Highline ISIS system was put in service to provide documented information about the complications.

Directed by Prof. Munir Elias

Team in action.

Starting from July-2007 all the surgical activities of Prof. Munir Elias will be guided under the electrophysiologic control of ISIS- IOM

ISIS-IOM Inomed Highline



Copyright [2014] [CNS Clinic - Jordan - Munir Elias]. All rights reserved